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Update busco to 5.7.0 (bioconda#46490)
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* Update busco to 5.7.0

* Constrain biopython; add patch

---------

Co-authored-by: Matthew Berkeley <42berkeley@cua.edu>
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2 people authored and Tim15-tech committed Mar 18, 2024
1 parent 950dcde commit 79dbad8
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Showing 2 changed files with 27 additions and 4 deletions.
23 changes: 23 additions & 0 deletions recipes/busco/0001-Set-conda-distribution.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
--- a/src/busco/run_BUSCO.py
+++ b/src/busco/run_BUSCO.py
@@ -121,18 +121,12 @@ class BuscoMaster:
logger.debug("File upload failed. Status code: {}".format(response.status))

def get_dist_info(self):
- if ( # todo: fix
- "conda" in __file__
- and os.environ("CONDA_DEFAULT_ENV")
- and os.environ("CONDA_PREFIX")
- ):
- self.run_data["distribution"] = "conda"
- elif os.path.exists("/.dockerenv"):
+ if os.path.exists("/.dockerenv"):
self.run_data["distribution"] = "docker"
elif os.path.exists("/.singularity.d"):
self.run_data["distribution"] = "singularity"
else:
- self.run_data["distribution"] = "manual"
+ self.run_data["distribution"] = "conda"

def get_download_url(self):
if self.config.getboolean("busco_run", "offline"):
8 changes: 4 additions & 4 deletions recipes/busco/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "busco" %}
{% set version = "5.6.1" %}
{% set sha256 = "1129d8dd1779455b77c47a926650e1974aaca58eeb9e6b3b6e4a706154ab2da8" %}
{% set version = "5.7.0" %}
{% set sha256 = "dbd9e07a5fb42583bd6ddbbfe06c420d5317a6f3698e6f4be0f53baa6c3ccc5e" %}

package:
name: busco
Expand All @@ -26,7 +26,7 @@ requirements:
- blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
- hmmer >=3.1b2 # sepp needs this version
- augustus >=3.3
- biopython
- biopython >=1.79
- prodigal
- sepp >=4.3.10
- dendropy <4.6.0 # necessary temporarily until SEPP updates their codebase or recipe
Expand All @@ -41,7 +41,7 @@ requirements:
- blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
- hmmer >=3.1b2 # sepp needs this version
- augustus >=3.3
- biopython
- biopython >=1.79
- r-base
- r-ggplot2 >=2.2.1
- prodigal
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